RetrogeneDB ID: retro_mmul_444

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:183023526..183024123(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: NIF3L1
• Ensembl ID: ENSMMUG00000006639
• Aliases: None
• Description: NIF3-like protein 1 [Source:RefSeq peptide;Acc:NP_001248662]

Sequence

>retro_mmul_444
ACCGAAGACCTGGACAAAGTCATGTCTGCAGTGAAAAAAAGTTGTGAATATTCCTTCTACTTCTTTGTCTGCTGGGATTG
ATGATGATAAACAAACATGGCTCAGTCTCAATTATACTCAGAAGACTTTGATGCAGGTAGTGGCTTTTCTCTCCCAGAAC
ATAAAATGGCATCAAAAGACTGAAATTTTGGACTGGAGAAGCCTTTGCTTCCACATAGTGGAATGGGATGGTTGTGCATA
CTGGATGAATCTATCTCCCTGACAACCATGACAGAGCAAATCAAAAGCCACTTAAAACTATCACATATGTGCTTAGTTCT
TAGAGTAGGGAGGACCTTAGAGTTCTAAAGTCAAAGTCATGGCCCTGTGTGCTGGTTCTGGGAGCAGCGTTCTGCAGAGT
ATGGAAGCTGATCTTTACCTCCCAGGTGGGATGTCTCATCATAATATTCTGAATGCTGCTTCCTAAGGAAGAAATGTCAC
CCTTTATGAACTCAGCAACACTGAATAAGGCTCTCTTTCTCACATTTGAGATATGCTGGGTGCTTACTTGAAGAGTAAGA
TTAATATTATCCTTCAGAGACAAGCAAGGACCCTCTT

Alignment

ORF - retro_mmul_444 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.01 %
• Parental protein coverage: 52.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TQALDKVMSAVKG-IGDVSVTSFSARFDNEEQTRISLNCTQKALMQVVDFLSQNKQLYQKTEILS-LEKP
          T..LDKVMSAVK........TS.SA..D...QT..SLN.TQK.LMQVV.FLSQN....QKTEIL..LEKP
Retrocopy TEDLDKVMSAVKK>VVNIPSTSLSAGIDDDKQTWLSLNYTQKTLMQVVAFLSQNIKWHQKTEILD<LEKP

Parental  LLLHTGMGRLCTLDESVSLATMIDRIKRHLKLSHIRLALGVGRTLE-SQVKVVALCAGSGSGVLQGVKAD
          LL.H.GMG.LC.LDES.SL.TM...IK.HLKLSH..L.L.VGRTLE.S.VKV.ALCAGSGS.VLQ...AD
Retrocopy LLPHSGMGWLCILDESISLTTMTEQIKSHLKLSHMCLVLRVGRTLE>SKVKVMALCAGSGSSVLQSMEAD

Parental  LYLTGEMSHHDILDAASQGINVILCEHSNTERGFLSDLRDMLGSHLENKINIIL-SETDRDPL
          LYL.G.MSHH.IL.AAS.G.NV.L.E.SNTE.G.LS...DMLG..L..KINIIL.SET..DPL
Retrocopy LYLPGGMSHHNILNAAS*GRNVTLYELSNTE*GSLSHI*DMLGAYLKSKINIIL<SETSKDPL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	11.09 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	11.11 RPM
SRP007412_cerebellum	0.00 RPM	12.40 RPM
SRP007412_heart	0.00 RPM	6.42 RPM
SRP007412_kidney	0.00 RPM	10.68 RPM
SRP007412_liver	0.00 RPM	5.82 RPM
SRP007412_testis	0.00 RPM	4.49 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_444 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_444 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_444 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_244

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000023186	1 retrocopy	retro_fcat_589,
Macaca mulatta	ENSMMUG00000006639	1 retrocopy	retro_mmul_444 ,
Nomascus leucogenys	ENSNLEG00000006935	1 retrocopy	retro_nleu_1504,
Oryctolagus cuniculus	ENSOCUG00000010667	16 retrocopies	retro_ocun_1105, retro_ocun_1534, retro_ocun_1539, retro_ocun_1691, retro_ocun_1692, retro_ocun_1710, retro_ocun_1729, retro_ocun_1749, retro_ocun_1789, retro_ocun_1828, retro_ocun_1837, retro_ocun_1841, retro_ocun_1846, retro_ocun_1847, retro_ocun_1854, retro_ocun_929,
Pongo abelii	ENSPPYG00000013063	1 retrocopy	retro_pabe_244,
Tupaia belangeri	ENSTBEG00000000704	1 retrocopy	retro_tbel_3512,